Job ID = 9157422 sra ファイルのダウンロード中... Completed: 127384K bytes transferred in 4 seconds (248477K bits/sec), in 1 file, 2 directories. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 5477242 spots for /home/okishinya/chipatlas/results/ce10/SRX2144172/SRR4188776.sra Written 5477242 spots total rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:15 5477242 reads; of these: 5477242 (100.00%) were unpaired; of these: 1034732 (18.89%) aligned 0 times 3858379 (70.44%) aligned exactly 1 time 584131 (10.66%) aligned >1 times 81.11% overall alignment rate Time searching: 00:01:15 Overall time: 00:01:15 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 319714 / 4442510 = 0.0720 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Tue, 27 Jun 2017 11:53:44: # Command line: callpeak -t SRX2144172.bam -f BAM -g ce -n SRX2144172.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2144172.05 # format = BAM # ChIP-seq file = ['SRX2144172.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 27 Jun 2017 11:53:44: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:53:44: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:53:44: # Command line: callpeak -t SRX2144172.bam -f BAM -g ce -n SRX2144172.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2144172.10 # format = BAM # ChIP-seq file = ['SRX2144172.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 27 Jun 2017 11:53:44: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:53:44: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:53:44: # Command line: callpeak -t SRX2144172.bam -f BAM -g ce -n SRX2144172.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2144172.20 # format = BAM # ChIP-seq file = ['SRX2144172.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 27 Jun 2017 11:53:44: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:53:44: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:53:50: 1000000 INFO @ Tue, 27 Jun 2017 11:53:51: 1000000 INFO @ Tue, 27 Jun 2017 11:53:51: 1000000 INFO @ Tue, 27 Jun 2017 11:53:56: 2000000 INFO @ Tue, 27 Jun 2017 11:53:57: 2000000 INFO @ Tue, 27 Jun 2017 11:53:57: 2000000 INFO @ Tue, 27 Jun 2017 11:54:02: 3000000 INFO @ Tue, 27 Jun 2017 11:54:03: 3000000 INFO @ Tue, 27 Jun 2017 11:54:03: 3000000 INFO @ Tue, 27 Jun 2017 11:54:08: 4000000 INFO @ Tue, 27 Jun 2017 11:54:09: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 11:54:09: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 11:54:09: #1 total tags in treatment: 4122796 INFO @ Tue, 27 Jun 2017 11:54:09: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:54:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:54:09: #1 tags after filtering in treatment: 4122796 INFO @ Tue, 27 Jun 2017 11:54:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:54:09: #1 finished! INFO @ Tue, 27 Jun 2017 11:54:09: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:54:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:54:09: #2 number of paired peaks: 2832 INFO @ Tue, 27 Jun 2017 11:54:09: start model_add_line... INFO @ Tue, 27 Jun 2017 11:54:09: 4000000 INFO @ Tue, 27 Jun 2017 11:54:09: start X-correlation... INFO @ Tue, 27 Jun 2017 11:54:09: end of X-cor INFO @ Tue, 27 Jun 2017 11:54:09: #2 finished! INFO @ Tue, 27 Jun 2017 11:54:09: #2 predicted fragment length is 138 bps INFO @ Tue, 27 Jun 2017 11:54:09: #2 alternative fragment length(s) may be 138 bps INFO @ Tue, 27 Jun 2017 11:54:09: #2.2 Generate R script for model : SRX2144172.10_model.r INFO @ Tue, 27 Jun 2017 11:54:09: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:54:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:54:10: 4000000 INFO @ Tue, 27 Jun 2017 11:54:10: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 11:54:10: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 11:54:10: #1 total tags in treatment: 4122796 INFO @ Tue, 27 Jun 2017 11:54:10: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:54:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:54:10: #1 tags after filtering in treatment: 4122796 INFO @ Tue, 27 Jun 2017 11:54:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:54:10: #1 finished! INFO @ Tue, 27 Jun 2017 11:54:10: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:54:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:54:11: #2 number of paired peaks: 2832 INFO @ Tue, 27 Jun 2017 11:54:11: start model_add_line... INFO @ Tue, 27 Jun 2017 11:54:11: start X-correlation... INFO @ Tue, 27 Jun 2017 11:54:11: end of X-cor INFO @ Tue, 27 Jun 2017 11:54:11: #2 finished! INFO @ Tue, 27 Jun 2017 11:54:11: #2 predicted fragment length is 138 bps INFO @ Tue, 27 Jun 2017 11:54:11: #2 alternative fragment length(s) may be 138 bps INFO @ Tue, 27 Jun 2017 11:54:11: #2.2 Generate R script for model : SRX2144172.20_model.r INFO @ Tue, 27 Jun 2017 11:54:11: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:54:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:54:11: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 11:54:11: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 11:54:11: #1 total tags in treatment: 4122796 INFO @ Tue, 27 Jun 2017 11:54:11: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:54:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:54:11: #1 tags after filtering in treatment: 4122796 INFO @ Tue, 27 Jun 2017 11:54:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:54:11: #1 finished! INFO @ Tue, 27 Jun 2017 11:54:11: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:54:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:54:11: #2 number of paired peaks: 2832 INFO @ Tue, 27 Jun 2017 11:54:11: start model_add_line... INFO @ Tue, 27 Jun 2017 11:54:12: start X-correlation... INFO @ Tue, 27 Jun 2017 11:54:12: end of X-cor INFO @ Tue, 27 Jun 2017 11:54:12: #2 finished! INFO @ Tue, 27 Jun 2017 11:54:12: #2 predicted fragment length is 138 bps INFO @ Tue, 27 Jun 2017 11:54:12: #2 alternative fragment length(s) may be 138 bps INFO @ Tue, 27 Jun 2017 11:54:12: #2.2 Generate R script for model : SRX2144172.05_model.r INFO @ Tue, 27 Jun 2017 11:54:12: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:54:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:54:21: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:54:22: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:54:22: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:54:27: #4 Write output xls file... SRX2144172.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:54:27: #4 Write peak in narrowPeak format file... SRX2144172.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:54:27: #4 Write summits bed file... SRX2144172.10_summits.bed INFO @ Tue, 27 Jun 2017 11:54:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1444 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:54:28: #4 Write output xls file... SRX2144172.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:54:28: #4 Write peak in narrowPeak format file... SRX2144172.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:54:28: #4 Write summits bed file... SRX2144172.20_summits.bed INFO @ Tue, 27 Jun 2017 11:54:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (561 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:54:29: #4 Write output xls file... SRX2144172.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:54:29: #4 Write peak in narrowPeak format file... SRX2144172.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:54:29: #4 Write summits bed file... SRX2144172.05_summits.bed INFO @ Tue, 27 Jun 2017 11:54:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2996 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。